undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'

Aaron Friesz
The machine I work on was recently upgraded.  When I compile against the HDF5 libraries that are installed on the system (1.18), I get these errors when trying to link.  Any help with figuring out what is wrong would be greatly appreciated.

--
Aaron Friesz


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'

Landon Clipp
Aaron,

Undefined references almost always mean that your compiler is not linking the libraries you need. This is not surprising considering your machine was recently upgraded. A little bit more information about your environment, compilation procedures etc would be helpful to determine why your libraries are not being properly included.

Regards,
Landon Clipp

On Mon, Nov 21, 2016 at 9:15 PM, Aaron Friesz <[hidden email]> wrote:
The machine I work on was recently upgraded.  When I compile against the HDF5 libraries that are installed on the system (1.18), I get these errors when trying to link.  Any help with figuring out what is wrong would be greatly appreciated.

--
Aaron Friesz


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'

Aaron Friesz
That is exactly what is happening.  Unfortunately I'm not certain of all the details as I don't maintain the install that is provided on the system.  I used to maintain my own version, but when the system was updated to BeeGFS it became easier to use the one provided. 

In terms of the specific linker call, in a simplified form, it looks like

mpicxx (object file list) (other libraries) -L(location of libhdf5.so) -lhdf5

So far as I can tell, the only undefined references are those that include H5P, I'm suspecting that they did not recompile the parallel version of the libraries.

On Tue, Nov 22, 2016 at 1:08 PM, Landon Clipp <[hidden email]> wrote:
Aaron,

Undefined references almost always mean that your compiler is not linking the libraries you need. This is not surprising considering your machine was recently upgraded. A little bit more information about your environment, compilation procedures etc would be helpful to determine why your libraries are not being properly included.

Regards,
Landon Clipp

On Mon, Nov 21, 2016 at 9:15 PM, Aaron Friesz <[hidden email]> wrote:
The machine I work on was recently upgraded.  When I compile against the HDF5 libraries that are installed on the system (1.18), I get these errors when trying to link.  Any help with figuring out what is wrong would be greatly appreciated.

--
Aaron Friesz


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.hdfgroup.org_mailman_listinfo_hdf-2Dforum-5Flists.hdfgroup.org&d=DgICAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Rx9txIqgEINHtVDIDfXdIw&m=aqPxJiCbdUQL5Kxkl4EOchQYc5_Apm8gW_wYitdnLxg&s=MgsqMuu5_8lJd0EDrmVR3kT_2giZR-JX-it2X2aCkag&e=
Twitter: https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_hdf5&d=DgICAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Rx9txIqgEINHtVDIDfXdIw&m=aqPxJiCbdUQL5Kxkl4EOchQYc5_Apm8gW_wYitdnLxg&s=-sTb4Ix6jLKp05hJeTt-gGsS_zh4tAnbNmBtQ6VQLNo&e=


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'

Landon Clipp

Without having access to your computer, it's difficult to tell exactly what is going on so I just need to give you maybe the insultingly obvious answers. You of course you want to check the paths to make sure all lib and include files are actually present. You might want to ask your system administrator to reinstall HDF libraries. I see you are doing dynamic linking, it is possible like you said that for some reason or another your libraries were not compiled. If that's truly the case, the only way to fix it is to recompile the libraries. That would have to be a question for your admin.

Sorry if this isn't terribly helpful, this issue isn't easily resolved without access to and familiarity with the system. I've dealt with undefined reference problems a lot and it always seems to be a different issue, but it of course is a symptom of the linker being unable to find the proper libraries or a botched installation of the libraries. My main advice would be to just make sure the libraries are in the directory you are telling the compiler they're at, or if your system has two versions of the HDF libraries and you're using the older one.

Another thing that I thought may be causing issues, I'm not familiar with mpicxx but I assume this is a gcc wrapper of some kind. I know at least with h4cc and h5cc, they are configured to include the hdf libraries upon install and if you move the library, h4cc/h5cc will be pointing to nothing and thus fail to include the library. I'm curious if mpicxx has a verbose compilation flag that would let you see what commands/flags it is giving to your native compiler.

Regards,
Landon


On Nov 22, 2016 7:13 PM, "Aaron Friesz" <[hidden email]> wrote:
That is exactly what is happening.  Unfortunately I'm not certain of all the details as I don't maintain the install that is provided on the system.  I used to maintain my own version, but when the system was updated to BeeGFS it became easier to use the one provided. 

In terms of the specific linker call, in a simplified form, it looks like

mpicxx (object file list) (other libraries) -L(location of libhdf5.so) -lhdf5

So far as I can tell, the only undefined references are those that include H5P, I'm suspecting that they did not recompile the parallel version of the libraries.

On Tue, Nov 22, 2016 at 1:08 PM, Landon Clipp <[hidden email]> wrote:
Aaron,

Undefined references almost always mean that your compiler is not linking the libraries you need. This is not surprising considering your machine was recently upgraded. A little bit more information about your environment, compilation procedures etc would be helpful to determine why your libraries are not being properly included.

Regards,
Landon Clipp

On Mon, Nov 21, 2016 at 9:15 PM, Aaron Friesz <[hidden email]> wrote:
The machine I work on was recently upgraded.  When I compile against the HDF5 libraries that are installed on the system (1.18), I get these errors when trying to link.  Any help with figuring out what is wrong would be greatly appreciated.

--
Aaron Friesz


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.hdfgroup.org_mailman_listinfo_hdf-2Dforum-5Flists.hdfgroup.org&d=DgICAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Rx9txIqgEINHtVDIDfXdIw&m=aqPxJiCbdUQL5Kxkl4EOchQYc5_Apm8gW_wYitdnLxg&s=MgsqMuu5_8lJd0EDrmVR3kT_2giZR-JX-it2X2aCkag&e=
Twitter: https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_hdf5&d=DgICAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Rx9txIqgEINHtVDIDfXdIw&m=aqPxJiCbdUQL5Kxkl4EOchQYc5_Apm8gW_wYitdnLxg&s=-sTb4Ix6jLKp05hJeTt-gGsS_zh4tAnbNmBtQ6VQLNo&e=


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'

Aaron Friesz
I just wanted to provide an update, in case anyone else has a similar issue.

The system I work on was updated and after the update, during linking of my program, I was getting 'undefined reference' errors for definitions that had specifically to do with parallel file I/O.  The issue was that there was a 'hidden' installation of hdf5 in my library path.  This installation didn't exist on the system before the update and it was not a parallel library.  So, to make a long story short, if you get 'undefined reference' for something you are certain should be in your library, go hunting in your library path for a rogue install of the same library.

Aaron


On Tue, Nov 22, 2016 at 6:34 PM, Landon Clipp <[hidden email]> wrote:

Without having access to your computer, it's difficult to tell exactly what is going on so I just need to give you maybe the insultingly obvious answers. You of course you want to check the paths to make sure all lib and include files are actually present. You might want to ask your system administrator to reinstall HDF libraries. I see you are doing dynamic linking, it is possible like you said that for some reason or another your libraries were not compiled. If that's truly the case, the only way to fix it is to recompile the libraries. That would have to be a question for your admin.

Sorry if this isn't terribly helpful, this issue isn't easily resolved without access to and familiarity with the system. I've dealt with undefined reference problems a lot and it always seems to be a different issue, but it of course is a symptom of the linker being unable to find the proper libraries or a botched installation of the libraries. My main advice would be to just make sure the libraries are in the directory you are telling the compiler they're at, or if your system has two versions of the HDF libraries and you're using the older one.

Another thing that I thought may be causing issues, I'm not familiar with mpicxx but I assume this is a gcc wrapper of some kind. I know at least with h4cc and h5cc, they are configured to include the hdf libraries upon install and if you move the library, h4cc/h5cc will be pointing to nothing and thus fail to include the library. I'm curious if mpicxx has a verbose compilation flag that would let you see what commands/flags it is giving to your native compiler.

Regards,
Landon


On Nov 22, 2016 7:13 PM, "Aaron Friesz" <[hidden email]> wrote:
That is exactly what is happening.  Unfortunately I'm not certain of all the details as I don't maintain the install that is provided on the system.  I used to maintain my own version, but when the system was updated to BeeGFS it became easier to use the one provided. 

In terms of the specific linker call, in a simplified form, it looks like

mpicxx (object file list) (other libraries) -L(location of libhdf5.so) -lhdf5

So far as I can tell, the only undefined references are those that include H5P, I'm suspecting that they did not recompile the parallel version of the libraries.

On Tue, Nov 22, 2016 at 1:08 PM, Landon Clipp <[hidden email]> wrote:
Aaron,

Undefined references almost always mean that your compiler is not linking the libraries you need. This is not surprising considering your machine was recently upgraded. A little bit more information about your environment, compilation procedures etc would be helpful to determine why your libraries are not being properly included.

Regards,
Landon Clipp

On Mon, Nov 21, 2016 at 9:15 PM, Aaron Friesz <[hidden email]> wrote:
The machine I work on was recently upgraded.  When I compile against the HDF5 libraries that are installed on the system (1.18), I get these errors when trying to link.  Any help with figuring out what is wrong would be greatly appreciated.

--
Aaron Friesz


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.hdfgroup.org_mailman_listinfo_hdf-2Dforum-5Flists.hdfgroup.org&d=DgICAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Rx9txIqgEINHtVDIDfXdIw&m=aqPxJiCbdUQL5Kxkl4EOchQYc5_Apm8gW_wYitdnLxg&s=MgsqMuu5_8lJd0EDrmVR3kT_2giZR-JX-it2X2aCkag&e=
Twitter: https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_hdf5&d=DgICAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Rx9txIqgEINHtVDIDfXdIw&m=aqPxJiCbdUQL5Kxkl4EOchQYc5_Apm8gW_wYitdnLxg&s=-sTb4Ix6jLKp05hJeTt-gGsS_zh4tAnbNmBtQ6VQLNo&e=


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.hdfgroup.org_mailman_listinfo_hdf-2Dforum-5Flists.hdfgroup.org&d=DgICAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Rx9txIqgEINHtVDIDfXdIw&m=7f4y0yurnqUfMPjJp6M4FJSE1u1BKk325rUMEf4MYt0&s=aoQyt_zxzDEcCowCiF9QpFItGpcNXp4PWbdjIg76HXg&e=
Twitter: https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_hdf5&d=DgICAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Rx9txIqgEINHtVDIDfXdIw&m=7f4y0yurnqUfMPjJp6M4FJSE1u1BKk325rUMEf4MYt0&s=I6JEOLD8U_pf2hnO0PWObLdEaLEGmof8Moevbx3tTzc&e=



--
Aaron Friesz
-----------------------------------------------------
University of Southern California
Department of Electrical Engineering
MicroPhotonic Devices Group
213 740 9208
[hidden email]

_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
Loading...